A bioactivity-guided chemical study of aerial parts of Croton ciliatoglanduliferus Ort. led to the isolation for the first time of the flavonoids retusin (5-hydroxy-3,7,3',4'-tetramethoxyflavone) (1) and pachypodol (5,4'-dihydroxy-3,7,3'-trimethoxyflavone) (2) from the n-hexane extract. Compounds 1 and 2 were separated by preparative thin-layer chromatography. Compound 2 was the most active compound on ATP synthesis inhibition. The I50 value was 51 micromolar. Pachypodol behaves as a Hill reaction inhibitor. It inhibited the uncoupled electron flow on photosystem II partial reaction from water to dichlorophenol indophenol (DCPIP) and from water to sodium silicomolybdate. However, the uncoupled partial reaction from diphenylcarbazide to DCPIP and the uncoupled photosystem I from DCPIPred to MV were not inhibited by 2. These results were corroborated by fluorescence decay data. Therefore, pachypodol inhibits the water-splitting enzyme activity. Compound 1 with a 4'-methoxy group was a weak inhibitor, indicating that the 4' free -OH group is important for strong inhibition.